With the rapid promotion of urbanization and the increase of extreme weather, the waterlogging problem affecting the urban safety is attracting the increasing public attention. Pudong New District is located in the eastern part of Shanghai with the uneven distribution of river channels, showing the characteristics of dense in the south and sparse in the north, dense outside the center and sparse in the center. The traditional drainage planning has been unable to fully meet the need of the current urban security. Combined with the characteristics of the city, the drainage and waterlogging control planning of Pudong New District adheres to the concept of "green-gray-blue" measures to explore the existing facilities deeply and reasonably solves the problem of source control and the combination of large and small drainage systems. By building a model to assess the risk of urban waterlogging, efficiently predict the regional flooding disasters and clarify the focus on upgrading and reconstructing the areas, the planning efficiency can be effectively improved and the planning effect can be timely fed back. The drainage system is upgraded and reconstructed by means of low-impact development of the existing system and the multi-purpose utilization of the existing drainage facilities. The ability of urban drainage and waterlogging prevention has been effectively improved, and some references are provided for the preparation of similar planning in the future.